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Synthetic patient data generated by Synthea can be loaded into i2b2. The Synthea SyntheticMass sample files have been converted to i2b2-ACT format, and scripts to load Synthea data from scratch are available here: https://github.com/i2b2/i2b2-synthea

Synthea Load Process

1. Set up an i2b2 project with the ACT ontology.
2. Either download the SyntheticMass 63k sample in i2b2 format from https://github.com/i2b2/i2b2-synthea/blob/main/syntheamass_63K_sample.zip, or follow the instructions below to load any Synthea dataset from scratch. This information can also be found on the Synthea-i2b2 Community Project page.

Loading Synthea data from scratch

1. Download SyntheticMass Data, Version 2 (24 May, 2017) 
   • (All data sets (1k, COVID 10k, COVID 100k) have been verified to work EXCEPT the 100k patients in the large SyntheticMass Version 2 download. 

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1. • The 100k patients in the large SyntheticMass Version 2 download needs an extra step to delete invalid records before import.In this case, download synthea_cleanup.pl to your disk, and then run "synthea_cleanup <directory-for-synthea-csv-files>" The fixed csv files will be in <directory-for-synthea-csv-files>/fixcsv

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1. • )
2. Set up an i2b2 project with the ACT ontology.
3. Download the scripts from https://github.com/i2b2/i2b2-synthea)
4. Run create_synthea_table_<your dbServertype>.sql in your project to create the Synthea tables.
5. Import the Synthea data you downloaded in step one into the Synthea tables in your project.
6. Load the i2b2-to-SNOMED table in this repository into your project. https://www.nlm.nih.gov/healthit/snomedct/us_edition.html
7. Click on the "Download SNOMED-CT to ICD-10-CM Mapping Resources" link to download. (You will need a UMLS account.)
8. Unzip the file
9. Import the TSV file into a table called SNOMED_to_ICD10 in your database.
10. In Postgres and Oracle, follow the additional instructions in the comments at the top of synthea_to_i2b2_<your dbServerType>.sql to clean up the date formatting.
11. Run synthea_to_i2b2_<your dbServertype>.sql to convert synthea data into i2b2 tables (this will truncate your existing fact and dimension tables!)
12. Replace references to i2b2metadata.dbo in the script. Use the database and schema where your ACT ontology tables are.

ACT Version-4 Ontology data load

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ACT4 data load process

1. Download the newinstall  zip package from https://www.i2b2.org/software/download.html?d=452
2. Extract the  metadata\act folder from the downloaded zip folder
3. Replace edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act  folder with extracted new act folder
4. Edit the  db.properties file in your metadata folder  to update the project properties to 'ACT' ; db.project=ACT
5. From the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata folder, run the ant command: ant -f data_build.xml db_metadata_load_data
6. This will execute the  SQL scripts from the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act\scripts\<db type> folder and create and load ACT4 Ontology metadata tables  
7. You can now verify the new Ontology  by logging into the webclient.

Security Enhancements

1. i2b2 has been made more secure by addressing parameterization and other potential vulnerabilities found in an internal a Veracode scan.
2. Log4J has been upgraded to the latest version. The following jars are updated in lib/axis2.war/WEB-INF/lib the folder:
   • log4j-api-2.17.1.jar
   • log4j-core-2.17.1.jar
   • log4j-jcl-2.17.1.jar

Improved db Upgrade Process

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